Ecological restoration in cities is problematic. The natural environment is radically altered with large areas of impervious surfaces, invasive species and a parallel artificial infrastructure for transporting water, waste and energy. There are also competing goals to meet the needs of people as identified in Official Community Plans. Cities are novel ecosystems and the restoration targets often do not align well with the natural ecosystems that historically existed in the area. The objective of this study is to use the University of Victoria campus as an example of urban restoration that incorporates novel ecosystems and takes a layered landscapes approach to address the complex socio-ecological histories of a site. Hobbs Creek and its ravine, Mystic Vale, are a particular focus. Instead of trying to restore the original fish-bearing stream and forest, the University of Victoria has used a novel ecosystem approach to set a suitable restoration target for an ecosystem that is capable of maturing, has a stable trajectory and is resilient. The university has an ongoing program of invasive species removal, reducing stream bank erosion and managing human impacts that is consistent with applying the layered landscapes concept, addressing the diverse values and visions of people as well as ecological integrity. In cities, the novel ecosystem approach acknowledges that complex socio-ecological histories of a site have shaped them over time and play a major role in determining a site’s future. Combining the layered landscapes perspective with the novel ecosystems concept as was done in this project is an effective approach to ecological restoration in cities.